Original broadcast: October 16, 2007
Ghost in Your Genes
Program Overview
NOVA explores how the epigenome—the body’s
complex chemical network that controls gene
expression—plays a role in human biological destiny.
The program:
• notes that, after mapping the human genome,
researchers wondered how so few genes could
account for so much diversity among the species.
• recounts how one scientist determined how the
deletion of a key sequence of DNA on human
chromosome 15 could lead to two different syndromes depending on
whether the deletion originated from the mother or the father.
• explains that this was the first human evidence that something other
than genes themselves could determine how genes are expressed.
• provides an animation of two ways that scientists think the epigenome
works to turn genes on and off.
• cites differentiation as an example of the epigenome at work—during
development, cells switch on or off to differentiate cell function; as the
cells divide they retain a memory of their cell type.
• notes that while the epigenome is normally incredibly stable, epigenetic
switches sometimes can be thrown and later lead to disease.
• looks at how the epigenetic profiles of two 66-year-old twins are very
different from that of two 6-year-old twins, suggesting that epigenetic
changes accumulate over time.
• presents several experiments with rats that reveal how the epigenome
works in an animal model.
• reports how epigenetic changes may promote disease by silencing tumor
suppressor genes or activating oncogenes.
• reviews a clinical trial in which half the patients recovered after being
treated with a drug designed to remove chemical tags silencing tumor
suppressor genes.
• presents the work of two scientists looking for an epigenetic influence
on autism.
• reports on a review of generations of historical records from a remote
Swedish village that suggests epigenetic changes may be passed down
through the generations.
Taping rights: Can be used up to one year after program is recorded off the air.
Before Watching
1 Epigenetic effects employ the
chemical mechanisms involved
with DNA. As a class, review the
following definitions: DNA,
chromosome, and genome (see Key
Terms on page 3). Use a model of
DNA to have students identify the
two strands that make up DNA,
the sugar-phosphate backbone, the
individual nucleotide bases, and
the nucleotide base pairs.
2 Review the concept of gene
expression with students. What is
it? (Gene expression is the ability
of a gene to produce a biologically
active protein.) To help students
understand this process, use the
graphic on page 2 to guide them
through the process of transcription and translation. Once you
have reviewed the process with
students, have them work in pairs
to transcribe and translate a gene
online at: learn.genetics.utah.edu/
units/basics/transcribe
AF TER WATCHING
1 Discuss the concept of epigenetics.
What is it? (Epigenetics is the
study of the modifications to genes,
such as by methylation, which do
not involve changing the underlying
DNA.) How does normal gene
expression differ from epigenetic
effects on the genome?
2 The program raises some social
and ethical implications regarding
epigenetic effects. While scientists
still don’t know exactly what affects
the epigenome or how it may be
passed down to future generations,
if lifestyle choices or environmental
effects are passed down, what
would students consider changing
about their current lifestyle for any
potential offspring they may have?
How certain would they need to be
that their epigenome was being
affected before they made the
change?
NOVA Teacher’s Guide
pbs.org/nova/genes
CLASSROOM ACTIVITY
Le arning Objec tive s
Activity Summary
Students model how scientists use DNA microarrays to determine levels
of gene expression in breast cancer patients, and then choose treatments
based on what they learn.
Students will be able to:
Materials for Teacher
• 1 white plastic ice cube tray per team, with at least 12 wells
• 500 mL vinegar
• 600 mL salt water (600mL water mixed with 6 Tbsp. salt)
• 500 mL of water
• pipettes
• small self-stick notes
• define DNA microarray and gene
expression.
• describe how microarrays are used
to determine gene expression.
• explain how understanding gene
expression can lead to improved
treatments for disease.
S TANDARDS
CONNEC TION
Materials for Each Team
• copy of “Checking Up on Genes” student handout
• copy of “How DNA Microarrays Work” student handout
• copy of “Gene Locations on Array” student handout
• copy of “Cancer Therapies” student handout
• 15 mL of phenolphthalein
• pipettes
The “Checking Up on Genes” activity
aligns with the following National
Science Education Standards (see
books.nap.edu/html/nses).
Background
Normal-functioning DNA codes for proteins through the processes of
transcription and translation. During transcription, one strand of DNA in a
cell’s nucleus is used to synthesize a strand of mRNA. After the mRNA is
produced, it moves into the cell’s cytoplasm. During translation, transfer
RNA (tRNA) and the cell’s ribosome work together to create a protein by
building a series of amino acid sequences specified by the nucleotides in
the mRNA. (The tRNA transports the amino acids while the ribosome
synthesizes them into proteins.) Proteins are involved in nearly every
aspect of the physiology and biochemistry of living organisms.
Grades 9 – 12
Life Science
The cell
The molecular basis of heredity
Science and Technology
Understandings about science and
technology
Science in Personal and Social
Perspectives
Personal and community health
Video is not required
for this activity.
the ribosome assembles
amino acids into proteins
RIBOSOME
A
DN
CELL
NUCLEUS
mRNA
CELL
CYTOPLASM
Ghost in Your Genes
NA
mR
when completed,
the protein is released
from the ribosome
transfer RNA
bringing an
amino acid
AMINO ACIDS
PROTEIN
NOVA Teacher’s Guide
pbs.org/nova/genes
CLASSROOM ACTIVITY (Cont.)
Ke y Terms
If a DNA molecule mutates, it may produce faulty proteins. If these
proteins are involved in controlling the processes of cell growth and
division, the mutation could trigger a cell to become abnormal and divide
uncontrollably. For many years, this was the only mechanism known
to cause cancer. Treatment of this type of cancer mainly relied on trying
to destroy the mutated cells.
chromosome: A tightly coiled
macromolecule of DNA and its
associated proteins. Chromosomes
contain many genes. Sexually
reproducing organisms have two
of each chromosome, one from each
parent. Organisms vary in the
number of chromosomes they have.
But researchers have now discovered that cancer can be triggered by
epigenetic changes—modifications to mechanisms associated with DNA
that alter gene expression without mutating the original DNA. These
changes are like switches turning genes on and off. Some epigenetic
effects turn on, or activate, genes that stimulate tumor growth; other
effects turn off, or silence, genes that would normally suppress tumor
growth. Since epigenetic changes do not alter the DNA sequence itself,
they hold the promise of being chemically reversed with drug (and
potentially nutritional) therapies.
Cancer may be caused by several different mutations or epigenetic
changes that cause genes to be expressed (turned on) and/or silenced
(turned off) when they should not be. By identifying which genes in the
cancer cells are working abnormally, doctors can better diagnose and
treat cancer.
One way scientists try to determine which genes are working abnormally
is to use a DNA microarray (see “How DNA Microarrays Work” student
handout for a complete description of how these arrays function). These
gene-expression “fingerprints” allow a doctor to determine both the
genes involved in a patient’s cancer and the possible reaction of each
patient to different drug treatments. This activity models how doctors use
microarrays to determine levels of gene expression in breast cancer
patients and then choose treatments based on what they learn.
Procedure
1 Before class, prepare enough microarrays for the number of teams you
will be organizing. The activity is designed for a tray with 16 wells. If
needed, you can delete columns 7 and 8 for trays with fewer wells.
Columns 1–6 are needed to complete the activity. The microarray
models you will be creating work on the basis of an acid, base, and
neutral. The solutions you prepare will be simulating the genes that are
already on a microarray before a patient’s cDNA is added. To prepare
the trays:
• Use a self-stick note to mark “TL” on the top left and “BR”
on the bottom right of each ice cube tray.
Ghost in Your Genes
complementary DNA (cDNA): A
single strand of DNA synthesized
in the lab to complement the bases
in a given strand of messenger RNA.
Complementary DNA represents the
parts of a gene that are expressed
in a cell to produce a protein.
deoxyribonucleic acid (DNA): A
double-stranded chain of nucleotides.
It carries a cell’s genetic information
and is found in the cells of all living
organisms. It is capable of selfreplication and the synthesis of RNA.
DNA microarray: A collection of
microscopic DNA spots attached to
a solid surface, such as glass, plastic,
or silicon chip, forming an array.
Scientists use DNA microarrays
to measure gene expression levels.
gene: The basic unit of inheritance.
A gene is made up of a sequence
of four different bases: A (adenine),
T (thymine), G (guanine), and
C (cytosine). The way that these
bases are combined determines the
gene's function. Genes control the
production of proteins.
gene expression: The process by
which the information encoded in
DNA is converted into a final gene
product (i.e., a protein or any of
several types of RNA).
genome: An organism’s basic
complement of DNA.
messenger RNA (mRNA): Serves as
a template for protein synthesis.
transfer RNA (tRNA): A set of RNA
molecules that transfer amino acids
to the ribosomes, where proteins are
assembled according to the genetic
code carried by mRNA. (Each type
of tRNA molecule is linked to a
particular amino acid.)
NOVA Teacher’s Guide
pbs.org/nova/genes
CLASSROOM ACTIVITY (Cont.)
• Put 15 mL of the pure vinegar, salt water solution, or water in the wells
according to the following key for each patient.
A = acid—vinegar (will stay clear)
B = base—salt water (will turn light pink)
N = neutral—water (will turn dark pink)
• Set up an equal number of Patient 1 and Patient 2 microarrays.
(The materials list specifies enough materials for up to eight arrays,
four of Patient 1 and four of Patient 2.)
Patient 1 Profile
1
2
3
4
5
6
7
8
A
A
A
B
B
N
B
N
A
B
N
A
N
A
B
N
B
N
Patient 2 Profile
1
2
3
4
5
6
7
8
A
N
B
N
B
A
B
A
N
B
A
B
A
B
B
N
B
A
2 Tell students they will by playing the role of oncologists specializing in
breast cancer and will be conducting microarray analyses on two newly
diagnosed breast cancer patients, Mrs. Jones and Mrs. Brown. Inform
students that Mrs. Jones is a 46-year-old African-American woman with
no family history of breast cancer and that Mrs. Brown is a 63-year-old
Caucasian woman who has had breast cancer on her mother’s side of
the family.
3 Organize students into teams. Assign half the students Patient 1 and
the other half Patient 2. Distribute copies of the student handouts
to each team. Review the activity with students.
4 Make sure students understand the flow of DNA to mRNA to protein
(see Background and Key Terms on page 3 for more information).
5 Have students read the “Checking Up on Genes” handout that explains
how they will do the activity. Then have them read the “How DNA
Microarrays Work” handout. Clarify any misunderstandings about any
terminology (see Key Terms on page 3) or the technology before
students work with their own microarray. (Note: For this activity, the
technique has been simplified.)
6 Distribute the trays you have prepared to each team, the
phenolphthalein, and the pipettes. Have students use the
phenolphthalein solution to add three drops to each of the spots on
their array. After all the spots have been treated, have students interpret
the results using the key on their "Gene Locations on Array" handout.
Than have each team record the result for its patient under each gene
name on the same handout.
Ghost in Your Genes
Safe ty Note
If students spill any of the
phenolphthalein on their skin, have
them immediately rinse it off
thoroughly with water. After
completion of the activity, rinse the
tubes and droppers with a weak acid,
such as vinegar.
NOVA Teacher’s Guide
pbs.org/nova/genes
CLASSROOM ACTIVITY (Cont.)
7 After teams have interpreted their results, have them use their
“Cancer Therapy Options” handout to determine which therapies might
be indicated for their patients. Point out that if the genes listed in the
“Do not use if” category for each therapy are expressed in the manner
indicated, then the patient would react badly or not respond to the
treatment. Ask students to use this information to determine which
treatments are safe to use for each patient. Have them record their
answers on the handout.
8 Discuss students’ results and answers to the questions on the
“Checking Up on Genes” student handout. If student DNA microarray
results differ, ask students why that might be. (Some reasons include
that the substances in the prepared microarray were not distributed evenly
or that students may have added different amounts of the substance
representing the cDNA.) Ask a representative from a Patient 1 team and
a representative from a Patient 2 team to report the treatment choices
for each patient. Are they the same? (No.) Ask students why, if both
women have breast cancer, the treatments are different. (The two
recommendations are different because even though both patients have
breast cancer, their gene expression profiles are different, and call for
different treatment regimens.)
9 To illustrate how chemicals in the body can control gene expression,
show students the portion of the program (2:32) that describes and
animates this process.
www.pbs.org/nova/teachers/activities/3413_genes.html#video
(QuickTime or Windows Media plug-in required.)
After students have viewed the video, ask them to describe two ways
researchers know how genes can be turned on and off. (Chemical tags,
such as methyl groups, can attach directly to DNA and switch genes on or
off, or tags can grab onto proteins called histones around which genes are
wrapped. Tightening or loosening the histones effectively hides [turns off ]
or exposes [turns on] the genes.)
10 As an extension, have students choose two of the genes in the
microarray profile and research what cell regulation processes the genes
control. Have students report to the class what they learned. Students
can find the genes in the National Center for Biotechnology Information
Gene database at
www.ncbi.nlm.nih.gov/sites/entrez?db=gene
Ghost in Your Genes
Classroom Activity Author
Margy Kuntz has written and edited
educational materials for 20 years.
She has authored numerous
educational supplements, basal text
materials, and trade books on
science, math, and computers.
NOVA Teacher’s Guide
pbs.org/nova/genes
ACTIVITY Answer
link s and book s
Gene Locations on Array
L ink s
Patient 1 Profile
NOVA—Ghost in Your Genes
www.pbs.org/nova/genes
1
2
3
4
5
6
7
8
A
ESR1
0
ABC-C6
0
BCL2
–
DPYD
–
TOP2A
+
GSTP1
–
CDC2
+
GATA3
0
Contains articles and multimedia
features to accompany the NOVA
program.
B
DHFR
+
EGFR
0
ERB-B2
+
ABC-B2
0
MT1
–
TGFB3
+
ANXA
–
GRB7
+
Backgrounder: Epigenetics and
Imprinted Genes
www.hopkinsmedicine.org/press/2002/
November/epigenetics.htm
Patient 2 Profile
1
2
3
4
5
6
7
8
A
ESR1
+
ABC-C6
–
BCL2
+
DPYD
–
TOP2A
0
GSTP1
–
CDC2
0
GATA3
+
B
DHFR
0
EGFR
–
ERB-B2
0
ABC-B2
–
MT1
–
TGFB3
+
ANXA
–
GRB7
0
Cancer Therapy Worksheet
Cyclophosphamide: Patient 1: yes; Patient 2: yes
Doxorubicin: Patient 1: yes; Patient 2: yes
Fluorouracil (5-FU): Patient 1: yes; Patient 2: no
Methotrexate: Patient 1: no; Patient 2: no
Paclitaxel: Patient 1: no; Patient 2: no
Tamoxifen: Patient 1: no; Patient 2: yes
Trastuzumab: Patient 1: yes; Patient 2: no
Key
+ = overexpressed
(dark pink)
– = underexpressed
(light pink)
0 = normal
(clear)
Student Handout Questions
1 Which treatment or treatments would you recommend for your patient?
Patient 1: a combination of cyclophosphamide, doxorubicin, fluorouracil,
and trastuzumab. Patient 2: a combination of cyclophosphamide,
doxorubicin, and tamoxifen.
2 Some genes, such as ERB-B2 and ESR1, have been found to be
associated with particular diseases or conditions such as cancer. Other
genes, such as the ABC-B2 gene, are not associated with a disease but
are involved in resistance to certain drugs or treatments. Why would it
be useful to test for the expression of genes like the ABC-B2 gene on a
microarray? If the gene is strongly expressed, it would mean that a
particular treatment might not work, or might even be harmful to the
person taking that drug.
Funding for NOVA is provided by The DOW Chemical
Company, David H. Koch, the Howard Hughes Medical
Institute, the Corporation for Public Broadcasting, and
public television viewers.
Provides a basic introduction to
epigenetics.
DNA Is Not Destiny
discovermagazine.com/2006/nov/cover
Explains some ways that epigenetic
changes unfold at the biochemical level
and details recent research in
epigenetics.
DNA Microarray
learn.genetics.utah.edu/units/biotech/
microarray
Offers a step-through interactive that
explains how microarrays work.
Epigenetics: The Science of Change
www.ehponline.org/members/2006/
114-3/focus.html
Provides an overview, with a diagram,
of the connection between epigenetic
factors and disease in humans.
What Is Epigenetics?
epigenome-noe.net/aboutus/
epigenetics.php
Offers a brief yet informative overview
of the field of epigenetics.
Book
The Epigenome: Molecular
Hide and Seek
by Stephan Beck and Alexander Olek
(editors).
Wiley, 2003.
Presents nine essays that cover the
historical origins of epigenetics and its
role in development, gene regulation,
disease, diet, and aging.
© 2007 WGBH Educational Foundation
Ghost in Your Genes
NOVA Teacher’s Guide
pbs.org/nova/genes
Ghost in Your Genes || Student Handout
Checking Up on Genes
You are oncologists specializing in breast cancer and
will be conducting a microarray analysis on one of two
newly diagnosed breast cancer patients, Mrs. Jones
and Mrs. Brown. You will be adding a solution to each
spot on the array that represents the complementary
DNA (cDNA) of your patient to determine her gene
expression profile. After you complete your
microanalysis, you will decide on her course of
treatment.
Procedure
1 Read your ”How DNA Microarrays Work” student
handout to learn what microarrays are used for and
how they work.
2 The plastic grid your teacher will give you
represents the microarray for your patient. Each
spot represents one gene. The solution represents
the cDNA of a cancer patient. Using the solution
your teacher has given you, use a pipette to add
three drops in each spot on the microarray for your
patient.
3 Once all the spots have been treated, use the key
on your “Gene Locations on Array” handout to
interpret your results. Then record the result for
your patient under each gene name on the same
handout.
4 After you have interpreted the results, use your
“Cancer Therapy Options” handout, which
describes several treatments for breast cancer. Use
the results of your microarray analysis to determine
which therapies might be indicated for your patient.
Then answer the questions on this page.
© 2007 WGBH Educational Foundation
Questions
Write your answers on a separate piece of paper.
1 Which treatment or treatments would you
recommend for your patient?
2 Some genes, such as ERB-B2 and ESR1, have been
found to be associated with particular diseases or
conditions such as cancer. Other genes, such as
the ABC-B2 gene, are not associated with a disease
but are involved in resistance to certain drugs or
treatments. Why would it be useful to test for the
expressions of genes like the ABC-B2 gene on a
microarray?
Ghost in Your Genes || Student Handout
How DNA Microarrays Work
In each type of cell, like a muscle cell or a skin cell,
different genes are expressed (turned on) or silenced
(turned off). If the cells that are turned on mutate,
they could—depending on what role they play in the
cell—trigger the cell to become abnormal and divide
uncontrollably, causing cancer.
By identifying which genes in the cancer cells are
working abnormally, doctors can better diagnose and
treat cancer. One way they do this is to use a DNA
microarray to determine the expression levels of
genes. When a gene is expressed in a cell, it generates
messenger RNA (mRNA). Overexpressed genes
generate more mRNA than underexpressed genes.
This can be detected on the microarray.
The first step in using a microarray is to collect
healthy and cancerous tissue samples from the
patient. This way, doctors can look at what genes are
turned on and off in the healthy cells compared to the
cancerous cells. Once the tissues samples are
obtained, the messenger RNA (mRNA) is isolated
from the samples. The mRNA is color-coded with
fluorescent tags and used to make a DNA copy (the
mRNA from the healthy cells is dyed green; the mRNA
from the abnormal cells is dyed red.)
The DNA copy that is made, called complementary
DNA (cDNA), is then applied to the microarray.
The cDNA binds to complementary base pairs in each
of the spots on the array, a process known as
hybridization. Based on how the DNA binds together,
each spot will appear red, green, or yellow (a
combination of red and green) when scanned with
a laser.
• A red spot indicates that that gene was strongly
expressed in cancer cells. (In your experiment these
spots will be dark pink.)
• A green spot indicates that that gene was strongly
repressed in cancer cells. (In your experiment these
spots will be light pink.)
• If a spot turns yellow, it means that that gene was
neither strongly expressed nor strongly repressed
in cancer cells. (In your experiment these spots will
be clear.)
• A black spot indicates that none of the patient’s
cDNA has bonded to the DNA in the gene located
in that spot. This indicates that the gene is inactive.
(All of the genes in your experiment are active.)
yellow
green
healthy
tissue sample
healthy cDNA
labeled green
mRNA is isolated
from sample and
used to make cDNA
the two samples
are mixed and
hybridized
to microarray
red
tumor
tissue sample
© 2007 WGBH Educational Foundation
cancerous cDNA
labeled red
A microarray is an orderly arrangement of rows and columns on a
surface like a glass slide. Each of the spots on an array contains
single-stranded DNA molecules that correspond to a single gene.
An array can contain a few, or thousands, of genes.
Ghost in Your Genes || Student Handout
Gene Locations on Array
The following charts show which genes are
represented by each spot on your array. Use the key
on this page to determine the expression level of each
gene for your patient. Then record whether each gene
was strongly expressed (+), strongly repressed (–), or
neither strongly expressed nor repressed (0)
underneath the name of each gene.
Patient 1 Profile
1
2
3
4
5
6
7
8
ESR1
ABC-C6
BCL2
DPYD
TOP2A
GSTP1
CDC2
GATA3
DHFR
EGFR
ERB-B2
ABC-B2
MT1
TGFB3
ANXA
GRB7
A
B
Patient 2 Profile
1
2
3
4
5
6
7
8
ESR1
ABC-C6
BCL2
DPYD
TOP2A
GSTP1
CDC2
GATA3
DHFR
EGFR
ERB-B2
ABC-B2
MT1
TGFB3
ANXA
GRB7
A
B
Key
+ = strongly expressed (dark pink)
– = strongly repressed (light pink)
0 = neither strongly expressed nor repressed (clear)
© 2007 WGBH Educational Foundation
Ghost in Your Genes || Student Handout
Cancer Therapies
Cyclophosphamide
Doxorubicin
Brand Names: Cytoxan, Neosar
Brand Names: Adriamycin, Rubex
What it is: chemotherapy drug
What it is: chemotherapy drug
How it works: Cyclophosphamide acts by transferring one
or more saturated carbon atoms to cellular
macromolecules. This damages the cancer cell DNA, and
slows or stops the growth of the cancer cells.
How it works: Doxorubicin inhibits RNA synthesis and
causes DNA strand breakage. This slows or stops the
growth of the cancer cells.
Do not use if one or more is true: ABC-B2 = +
GSTP1 = +
MT1 = +
Safe to use for:
Patient 1 yes no
Do not use if one or more is true: EGFR = +
ABC-C6 = +
Safe to use for:
Patient 1 yes no
Patient 2 yes no
Patient 2 yes no
Fluorouracil (5-FU)
Methotrexate
Brand Name: Adrucil
Brand Names: Mexate, Folex
What it is: chemotherapy drug
What it is: chemotherapy drug
How it works: Fluorouracil binds with and deactivates a
key enzyme (thymidylate synthetase) in thymidine
biosynthesis. This slows or stops the growth of the cancer
cells.
How it works: Methotrexate binds to and inactivates the
enzyme dihydrofolate reductase (DHFR), and inhibits the
synthesis of purine and pyrimidine. This prevents the
growth of cancer cells.
Do not use if one or more is true: EGFR = +
BCL2 = +
DPYD = +
Do not use if one or more is true: BCL2 = +
DHFR = +
Safe to use for:
Patient 1 yes no
Safe to use for:
Patient 1 yes no
Patient 2 yes no
Patient 2 yes no
Paclitaxel
Tamoxifen
Brand Name: Taxol
Brand Name: Nolvadex
What it is: chemotherapy drug
What it is: hormone (antiestrogen)
How it works: Paclitaxel binds to tubulin and blocks cell
division. This slows or stops the growth of cancer cells.
How it works: Tamoxifen binds to the estrogen receptor,
preventing cell growth. It also affects the cycling of the cell
in the natural cell cycle.
Do not use if one or more is true: BCL2 = +
ERB-B2 = +
Safe to use for:
Patient 1 yes no
Patient 2 yes no
Do not use if one or more is true: ESR1 = 0 or –
ERB-B2 = +
Safe to use for:
Patient 1 yes no
Patient 2 yes no
Brand Name: Herceptin
What it is: monoclonal antibody
How it works: Herceptin binds to the ERB-B2 growth factor
receptor and prevents the cell from dividing.
Do not use if one or more is true: ERB-B2 = 0 or –
Safe to use for:
Patient 1 yes no
Patient 2 yes no
© 2007 WGBH Educational Foundation
Trastuzumab